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- PDB-7epr: Partial Consensus L-threonine 3-dehydrogenase (C-Change) -

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Database: PDB / ID: 7epr
TitlePartial Consensus L-threonine 3-dehydrogenase (C-Change)
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / L-threonine 3-dehydrogenase / artificial protein
Function and homology information
Biological speciessynthetic construct (unknown)
AuthorsKozuka, K. / Nakano, S. / Asano, Y. / Ito, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K14391 Japan
Japan Society for the Promotion of Science (JSPS)17H06169 Japan
Japan Science and TechnologyJPMJPR20AB Japan
CitationJournal: Biochemistry / Year: 2021
Title: Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations.
Authors: Kozuka, K. / Nakano, S. / Asano, Y. / Ito, S.
DepositionApr 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release

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Deposited unit
A: L-threonine 3-dehydrogenase
B: L-threonine 3-dehydrogenase
C: L-threonine 3-dehydrogenase
D: L-threonine 3-dehydrogenase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)151,7998
A: L-threonine 3-dehydrogenase
B: L-threonine 3-dehydrogenase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)75,8994
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-26 kcal/mol
Surface area22560 Å2
C: L-threonine 3-dehydrogenase
D: L-threonine 3-dehydrogenase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)75,8994
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-28 kcal/mol
Surface area21620 Å2
Unit cell
Length a, b, c (Å)149.019, 58.474, 138.130
Angle α, β, γ (deg.)90.000, 92.234, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions


Noncrystallographic symmetry (NCS)NCS domain:

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A5 - 314
221B5 - 314
332A5 - 314
442C5 - 314
553A7 - 312
663D7 - 312
774B5 - 314
884C5 - 314
995B7 - 312
10105D7 - 312
11116C7 - 312
12126D7 - 312

NCS ensembles :
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12


#1: Protein
L-threonine 3-dehydrogenase /

Mass: 37286.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (unknown) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide

Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop
Details: 20% [w/v] PEG 3350, 0.2M sodium phosphate monobasic monohydrate

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→46 Å / Num. obs: 412432 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.559 / Num. unique obs: 8720 / CC1/2: 0.847


XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMX
Resolution: 2.2→46 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.931 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / ESU R: 0.345 / ESU R Free: 0.239
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2582 3100 5.103 %
Rwork0.2083 57650 -
all0.211 --
obs-60750 99.859 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.019 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å2-0 Å20.062 Å2
2--0.075 Å20 Å2
3----0.084 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9335 0 176 375 9886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139751
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179078
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.64613303
X-RAY DIFFRACTIONr_angle_other_deg1.271.57620931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9151190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58422.232457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.304151565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1631556
X-RAY DIFFRACTIONr_chiral_restr0.0730.21331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022166
X-RAY DIFFRACTIONr_nbd_refined0.2020.21956
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.28676
X-RAY DIFFRACTIONr_nbtor_refined0.1620.24786
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2507
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2340.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.229
X-RAY DIFFRACTIONr_nbd_other0.2510.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3510.29
X-RAY DIFFRACTIONr_mcbond_it4.5074.8564790
X-RAY DIFFRACTIONr_mcbond_other4.5034.8554789
X-RAY DIFFRACTIONr_mcangle_it6.4077.2645970
X-RAY DIFFRACTIONr_mcangle_other6.4087.2655971
X-RAY DIFFRACTIONr_scbond_it4.415.1224961
X-RAY DIFFRACTIONr_scbond_other4.4095.1224962
X-RAY DIFFRACTIONr_scangle_it6.4847.5327333
X-RAY DIFFRACTIONr_scangle_other6.4847.5327334
X-RAY DIFFRACTIONr_lrange_it9.25455.90311153
X-RAY DIFFRACTIONr_lrange_other9.26155.911081
X-RAY DIFFRACTIONr_ncsr_local_group_10.0980.059835
X-RAY DIFFRACTIONr_ncsr_local_group_20.10.059813
X-RAY DIFFRACTIONr_ncsr_local_group_30.1020.059052
X-RAY DIFFRACTIONr_ncsr_local_group_40.1040.059837
X-RAY DIFFRACTIONr_ncsr_local_group_50.0980.059091
X-RAY DIFFRACTIONr_ncsr_local_group_60.1070.059015
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.097560.05008
12BX-RAY DIFFRACTIONLocal ncs0.097560.05008
23AX-RAY DIFFRACTIONLocal ncs0.100010.05008
24CX-RAY DIFFRACTIONLocal ncs0.100010.05008
35AX-RAY DIFFRACTIONLocal ncs0.101960.05008
36DX-RAY DIFFRACTIONLocal ncs0.101960.05008
47BX-RAY DIFFRACTIONLocal ncs0.10410.05008
48CX-RAY DIFFRACTIONLocal ncs0.10410.05008
59BX-RAY DIFFRACTIONLocal ncs0.097620.05008
510DX-RAY DIFFRACTIONLocal ncs0.097620.05008
611CX-RAY DIFFRACTIONLocal ncs0.106810.05008
612DX-RAY DIFFRACTIONLocal ncs0.106810.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.3472190.2834191X-RAY DIFFRACTION98.3058
2.257-2.3190.3262350.274073X-RAY DIFFRACTION100
2.319-2.3860.2952360.2464013X-RAY DIFFRACTION100
2.386-2.460.32030.2423923X-RAY DIFFRACTION100
2.46-2.540.3131860.2423797X-RAY DIFFRACTION100
2.54-2.6290.2952010.233658X-RAY DIFFRACTION100
2.629-2.7290.2751990.233519X-RAY DIFFRACTION100
2.729-2.840.2831960.2373385X-RAY DIFFRACTION100
2.84-2.9660.2911960.2273294X-RAY DIFFRACTION100
2.966-3.1110.2891500.2313131X-RAY DIFFRACTION100
3.111-3.2790.2781590.2162973X-RAY DIFFRACTION100
3.279-3.4780.261650.2162829X-RAY DIFFRACTION100
3.478-3.7180.2321430.1992650X-RAY DIFFRACTION100
3.718-4.0150.2111330.1792467X-RAY DIFFRACTION100
4.015-4.3980.2051080.1732301X-RAY DIFFRACTION100
4.398-4.9170.2261230.1632079X-RAY DIFFRACTION100
4.917-5.6760.241800.1811847X-RAY DIFFRACTION100
5.676-6.9490.226690.1871576X-RAY DIFFRACTION100
6.949-9.8150.197630.1651239X-RAY DIFFRACTION100
9.815-460.282360.257705X-RAY DIFFRACTION98.8

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